COPYRIGHT AND CITATION CONSIDERATIONS FOR THIS THESIS/ DISSERTATION o Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. o NonCommercial — You may not use the material for commercial purposes. o ShareAlike — If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original. How to cite this thesis Surname, Initial(s). (2012). Title of the thesis or dissertation (Doctoral Thesis / Master’s Dissertation). Johannesburg: University of Johannesburg. Available from: http://hdl.handle.net/102000/0002 (Accessed: 22 August 2017). A redescription of groundwater amphipods (Crangonyctoidea: Sternophysingidae) from karstic aquifers in Gauteng, South Africa By Kimberley Anne Murray DISSERTATION Submitted in fulfilment of the requirements for the degree MASTER OF SCIENCE in ZOOLOGY in the FACULTY OF SCIENCE UNIVERSITY OF JOHANNESBURG November 2020 Supervisor: Prof. J. F. Durand Table of Contents Table of Contents ..................................................................................................... i List of Figures ........................................................................................................ iv List of Tables .......................................................................................................... ix Acknowledgements ................................................................................................. x Abstract .................................................................................................................. xi Chapter 1. Introduction ........................................................................................ 1 1.1 Introduction ............................................................................................. 1 1.2 Aim ......................................................................................................... 5 Chapter 2. Groundwater ....................................................................................... 6 2.1 Introduction ............................................................................................. 6 2.2 Karst ........................................................................................................ 7 2.2.1 Karst Formation .................................................................................. 7 2.2.2 Drainage in karst landscapes ............................................................. 10 2.2.3 Karst in South Africa ......................................................................... 11 2.3 Groundwater in South Africa ................................................................ 13 2.3.1 Types of aquifers ............................................................................... 13 2.3.2 Threats to groundwater in South Africa ............................................ 14 2.4 Conclusion ............................................................................................ 15 Chapter 3. The hypogean environment .............................................................. 16 3.1 Introduction ........................................................................................... 17 3.2 Amphipods ............................................................................................ 19 3.2.1 Taxonomy.......................................................................................... 20 Page | i 3.3 Sternophysingids ................................................................................... 21 3.3.1 Past research on sternophysingids .................................................... 23 3.3.2 Calceoli ............................................................................................. 26 3.3.3 The evolutionary history of sternophysingids ................................... 32 3.4 Threats to amphipods ............................................................................ 34 3.5 Conclusion ............................................................................................ 34 Chapter 4. The colonisation of continental groundwater ................................... 36 4.1 Models of colonisation .......................................................................... 36 4.2 Problem with predictions ...................................................................... 38 4.3 Gondwanan origins ............................................................................... 39 Chapter 5. Research design and methodology .................................................. 42 5.1 Aim and objectives ............................................................................... 42 5.2 Site selection and sample collection ..................................................... 42 5.2.1 Site selection ..................................................................................... 42 5.2.2 Sample collection .............................................................................. 43 5.3 Ethical considerations ........................................................................... 43 5.4 Illustrations and descriptions ................................................................ 44 5.5 Scanning electron microscopy .............................................................. 44 5.6 DNA extraction ..................................................................................... 45 5.7 Polymerase chain reactions (PCRs) ...................................................... 46 5.8 Genetic analysis .................................................................................... 46 Chapter 6. Results .............................................................................................. 47 6.1 Sternophysinx filaris Holsinger and Straskraba, 1973 .......................... 47 ii 6.2 Sternophysinx calceola Holsinger, 1992 ............................................... 57 6.3 DNA extraction and PCR ...................................................................... 66 6.4 Genetic Analysis ................................................................................... 66 Chapter 7. Discussion ........................................................................................ 73 7.1 Introduction ........................................................................................... 73 7.2 Groundwater implications ..................................................................... 74 7.2.1 Conservation ..................................................................................... 75 7.3 Phylogenetic implication ...................................................................... 76 7.4 Population Structure .............................................................................. 79 7.4.1 Ecotones ............................................................................................ 80 7.5 Threats to amphipods ............................................................................ 81 7.6 Limitations and recommendations ........................................................ 83 Chapter 8. Conclusion ........................................................................................ 85 Figures ................................................................................................................. 106 iii List of Figures Figure 1. Map showing the location of the sample sites, Sterkfontein Cave, Grobler’s Cave, Bakwena Cave and Matlapitse Cave, all within the Chuniespoort dolomites of the Transvaal Supergroup (Late Archaean-Early Proterozoic) shown in blue. The Ecca Group (Lower Permian) is shown in red. Much of the vacant white region in the centre of the map is composed of the Bushveld Igneous Complex (Palaeoproterozoic). Sternophysingid amphipods are now known from habitats in all of these geological rock types. ................................................................ 12 Figure 2. Sternophysinx filaris, whole specimen (5.9 mm), Grobler’s Cave, South Africa. ........................................................................................................................................... 48 Figure 3. Scanning electron micrograph of Sternophysinx filaris collected from Sterkfontein Cave. ............................................................................................ 48 Figure 4. Sternophysinx filaris antenna 1 (upper right) and antenna 2 (lower left). Peduncles are numbered 1, 2 and 3 on antenna 1, and 4, 5 and 6 on antenna 2. .......................................................................................................................... 49 Figure 5. Scanning electron micrograph of Sternophysinx filaris specimen collected from Sterkfontein Cave. Peduncles of antennae1 and 2 shown as well as gland cones and palp of the mandible. .................................................................................. 49 Figure 6. Sternophysinx filaris upper (left) and lower lip (right) ..................................... 50 Figure 7. Sternophysinx filaris maxilla 1, showing inner lobe (left), outer lobe (right), and palp (top). .......................................................................................................... 50 Figure 8. Sternophysinx filaris maxilla 2 showing inner lobe (left) and outer lobe (right). ..........................................................................................................................................